ASICS: Automatic Statistical Identification in Complex Spectra

In GaelleLefort/ASICS: Automatic Statistical Identification in Complex Spectra

Description

Quantification of 1D 1H NMR spectra with ASICS method using a library of pure metabolite spectra. The method is presented in Tardivel et al. (2017).

Usage

ASICS(
  spectra_obj,
  exclusion.areas = matrix(c(4.5, 5.1), ncol = 2),
  max.shift = 0.02,
  pure.library = NULL,
  threshold.noise = 0.02,
  combine = TRUE,
  seed = 1234,
  ncores = 1,
  verbose = TRUE
)

Arguments

spectra_obj	An object of class Spectra obtained with the function createSpectra.
exclusion.areas	Definition domain of spectra that has to be excluded for the quantification (ppm). By default, the water region is excluded (4.5-5.1 ppm).
max.shift	Maximum chemical shift allowed (in ppm). Default to 0.02.
pure.library	An object of class PureLibrary containing the reference spectra (pure metabolite spectra). If NULL, the library included in the package (that contains 191 reference spectra) is used.
threshold.noise	Threshold for signal noise. Default to 0.02.
combine	Logical. If TRUE, information from all spectra are taken into account to align individual library.
seed	Random seed to control randomness in the algorithm (used in the estimation of the significativity of a given metabolite concentration).
ncores	Number of cores used in parallel evaluation. Default to 1.
verbose	A boolean value to allow print out process information.

Value

An object of type ASICSResults containing the quantification results.

Note

Since version 2.3.1 small changes were applied in order to improve the speed of metabolite selection algorithm. To reproduce previous results, you have to use an older version.

References

Tardivel P., Canlet C., Lefort G., Tremblay-Franco M., Debrauwer L., Concordet D., Servien R. (2017). ASICS: an automatic method for identification and quantification of metabolites in complex 1D 1H NMR spectra. Metabolomics, 13(10): 109. https://doi.org/10.1007/s11306-017-1244-5

See Also

ASICSResults pure_library createSpectra

Examples

# Import data and create object
current_path <- system.file("extdata", package = "ASICS")
spectra_data <- importSpectra(name.dir = current_path,
                     name.file = "spectra_example.txt", type.import = "txt")
spectra_obj <- createSpectra(spectra_data)

# Estimation of relative quantifications
to_exclude <- matrix(c(4.5, 10), ncol = 2)
resASICS <- ASICS(spectra_obj, exclusion.areas = to_exclude, combine = FALSE)

GaelleLefort/ASICS documentation built on July 19, 2020, 2:08 p.m.